The company resigned ahead of potential changes in PhRMA's membership criteria, which should be released in May. Earlier in April, Mallinckrodt Pharmaceuticals also resigned from the lobbying group.

PhRMA's been making a push to improve the perception of drug companies — highlighting innovation in the industry — after two years of bad press about skyrocketing prices and gouging by companies that acquire old drugs and don't spend much on research.

PhRMA has made a point of distinguishing itself from companies that have drawn outrage about drug prices. When Valeant Pharmaceuticals was under fire for its practice of acquiring medications and drastically raising their prices, the group wrote in an October 2015 blog post that, the "strategy is more reflective of a hedge fund than an innovative biopharmaceutical company."

And the group distanced itself from Marathon after the company got FDA approval for a drug to treat Duchenne muscular dystrophy. Once approved, Marathon set the list price at $89,000. In other countries, the price for the same drug is as low as $1,200 a year.

"We are pleased Marathon decided to pause the launch of their medicine to solicit additional input from patients and other stakeholders," PhRMA said in a statement to Endpoints after the launch was halted. "Their recent actions are not consistent with the mission of our organization."